read_dataset_csv: Reads a dataset from CSV files

In specmine: Metabolomics and Spectral Data Analysis and Mining

Reads a dataset from CSV files

Description

Reads a dataset from a CSV file containing the data matrix and, optionally, a second CSV file containing metadata.

Usage

read_dataset_csv(
  filename.data,
  filename.meta = NULL,
  type = "undefined",
  description = "",
  label.x = NULL,
  label.values = NULL,
  sample.names = NULL,
  format = "row",
  header.col = TRUE,
  header.row = TRUE,
  sep = ",",
  header.col.meta = TRUE,
  header.row.meta = TRUE,
  sep.meta = ","
)

Arguments

filename.data	Path to the CSV file containing the data matrix.
filename.meta	Optional path to the CSV file containing metadata.
type	Character string describing the dataset type.
description	Character string with a dataset description.
label.x	Optional x-axis label.
label.values	Optional value labels.
sample.names	Optional sample names.
format	Data layout format, either "row" or "col".
header.col	Logical; whether the data file has a header row.
header.row	Logical; whether the data file has a row names column.
sep	Field separator used in the data file.
header.col.meta	Logical; whether the metadata file has a header row.
header.row.meta	Logical; whether the metadata file has a row names column.
sep.meta	Field separator used in the metadata file.

Value

An object of class dataset created from the input files. This object contains the imported data matrix and, if provided, the sample metadata, together with dataset-level information such as type, description, labels, and sample names. The returned object is intended to be used as input to downstream processing and analysis functions in the package.

Examples

data_file <- tempfile(fileext = ".csv")
meta_file <- tempfile(fileext = ".csv")

data_in <- data.frame(
  x1 = c(1.1, 2.2, 3.3),
  x2 = c(4.4, 5.5, 6.6),
  row.names = c("s1", "s2", "s3")
)
metadata_in <- data.frame(
  class = c("A", "B", "A"),
  row.names = c("s1", "s2", "s3")
)

utils::write.csv(data_in, data_file)
utils::write.csv(metadata_in, meta_file)

dataset <- read_dataset_csv(
  filename.data = data_file,
  filename.meta = meta_file,
  format = "row",
  header.row = TRUE,
  header.row.meta = TRUE
)
class(dataset)

specmine documentation built on Aug. 5, 2026, 5:06 p.m.